R2 and Cytoscape: Inferring gene targets by graph based integration and analysis of molecular biological data

Piet Molenaar

Academic Medical Center, University of Amsterdam, the Netherlands

Recipe

Cytoscape version: 2.4 - 2.6

Plugins to Load: BiNGO (Piet: provide link), NetMatch (http://baderlab.org/Software/NetMatch)

GUI steps:

  1. Open website: http://hgserver1.amc.nl/cgi-bin/r2/main.cgi

  2. Logon with: un pw -> if problem switch to ppt (Piet: todo provide restricted access logon)

  3. Click Timeseries: a panel provides you with three choices;

  4. Select TableBuilder:

  5. Choose cellline imr
  6. Choose Notch1
  7. tbc

Data Files: Notch timeseries (Piet: refine this)

Presentation:

Webstart: Time permitting

Video: Time permitting

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

MoinMoin Appliance - Powered by TurnKey Linux